The 55 Pontiac 3 speed is a GM "5 bolt" (number of bolts on the cover plate) gearbox and your 56 Special should have a "6 bolt". You can use the Pontiac gearbox if you re-drill your bellhousing for the 5 bolt pattern. I did this when I converted a 52 Buick 70 to manual shift (using a 52 series 50 gearbox) and it worked fine. Keep in mind that the 5 bolt box isn't as strong as the 6 bolt and you may have to modify your shift linkage slightly.
Three other possibilities: Look for a 54 or 55 Buick 40 bellhousing. These cars came stock with a 5 bolt gearbox and the bellhousing will fit your 56 engine. Alternatively, if you can find a 56 or 57 Pontiac gearbox, that is a 6 bolt and it will fit your present bellhousing. Lastly, 51-64 full-size Oldsmobiles (except 64 Jetstar 88) used the 6 bolt gearbox, but these will require a bit more work. The Olds input shaft has a 1-1/4" spline instead of 1-1/8" like Buick and Pontiac. You can replace your present clutch disc with a 1-1/4" spline disc, but I think the release bearing support is also slightly larger diameter on the Olds, which means you might have to cobble a release bearing setup.
All of the above assumes that you want to replace your torque tube with an open drive. If that's not your intended goal, just keep on looking for another Buick gearbox instead. It will be a lot less work to get your car back on the road if you keep the torque tube.
Ray